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protein identification problem

From: Ken I Fukuda <fukuda-cbrc@aist.go.jp>
Date: Wed, 29 Jun 2005 11:37:59 -0400
To: public-semweb-lifesci@w3.org
Message-Id: <20050628132552.35A5.FUKUDA-CBRC@aist.go.jp>

Hi all,

In the ISMB Semantic web for Life Science BOF,
an issue was raised about the ambiguity of how people
refer to a protein in the literature.

For example, let's say, you find a description such as
"JNK activates JUN" but acctually this "JNK" stands for
a bunch of proteins ("concrete entities") and JUN
also stands for a set of proteins.

This isssue is known as the "generic entitity" problem.
If you read the literature, you typically encounter these
"generic protein" names.
And there should be a mechanism that tells you how many
proteins you have for each generic name.

An ontology for generic/concrete protein names, called
"MoleculeRole Ontology" is available from
http://www.inoh.org/ontology-viewer/.
Actually, it is a DAG structured controled vocabulary (CV).
The current version covers about 4400 Uniprot IDs which means
that the CV defines generic/concrete protein relations for
more than 4400 concrete proteins.

The CV is available in OBO format (Gene Ontology native format).
http://www.inoh.org/download.html

PS.
There are some OBO->OWL converters, but some argued they didn't
fit their needs. It would be nice to know how people like to
convert an OBO ontology into an OWL file.

Best,
Ken

--------------------------------------------- 
Ken Ichiro Fukuda, Ph.D.
Computational Biology Research Center (CBRC)
National Institute of 
Advanced Industrial Science and Technology (AIST)
AIST Tokyo Waterfront Bio-IT Research Bldg. 10F
2-42 Aomi, Koutou-ku, Tokyo 135-0064 JAPAN
Phone: +81-3-3599-8049  FAX: +81-3-3599-8081
fukuda-cbrc@aist.go.jp / fukuda_cbrc@yahoo.co.jp
     - http://www.cbrc.jp/~fukuda/index.html
- INOH Pathway Database Project -
     - Integrating Network Objects with Hierarchies
     - http://www.inoh.org
Received on Thursday, 30 June 2005 02:20:34 UTC

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